I'm a big fan of CLI accounting software (Ledger, Beancount and hledger) for my personal finances. Allows you to use a plain text file for recording your financial data. If you live a large percentage of your life in a command line environment, and you like your life scriptable, check it out. I personally use hledger, but would recommend that folks check out http://plaintextaccounting.org/ for a great overview of all cli accounting packages.

I love the command line, and really wanted to love Ledger, but found that manual transaction entry for it (even using Emacs) was far inferior to Gnucash, which does far more powerful autocompletion on previous entries. This makes Ledger impractical for manually entering thousands of transactions, which I had to do.

I also tried some GUI interface to Ledger that was supposed to be better in this respect, but couldn't get it to work.

My "entry" work is modifying some categories that it gets wrong.

I don't fully understand your situation, so I'm not expecting it necessarily solve your entry problems. I'm only raising awareness.